In general, you should only use .htaccess files when you don't have access to the main server configuration file.

This is on shared hosting so I don't have access to the server configuration file!

That's no reason to stop reading.

Depending on how your shared hosting is set up, there may still be a way to place files outside the reach of the webserver. My shared hoster gives me some filespace somewhere on a unix system, and has a configuration panel that allows to assign any directory of that filespace to any domain hosted there. So I made a few subdirectories and used a subdirectory per domain. Other subdirectories are still unassigned, can not be accessed via HTTP, and thus are perfect for libraries and configuration files.

Alexander